You are talking about GPU slots obviously, so you seem to have gotten confused. The AGP graphics slot was the upgrade from PCI for GPUs. PCI-E
(which is PCI-Express) is the newest, most advanced graphics slot.
In order to use a PCI-E GPU, you will need a motherboard that has a PCI-E slot on it. These are extremely common, and one I would recommend is the MSI K8N Neo4-F http://www.newegg.com/Product/Produc...82E16813130491
Note that is a slot 939, which is for AMD 64 processors. If you have an Intel processor, take a look at Newegg for a motherboard for it.
You should definetly go for a PCI-E motherboard and GPU if you can. It installs basically the same (however newer GPUs require a connection from the card to the PSU) and drivers run and install the same.